rs1478224

Variant names:

• chr4-167515850-C-A
• rs1478224

Variant summary

Our verdict is Benign. The variant received -9 ACMG points: 0P and 9B. BP4 BA1

The variant allele was found at a frequency of 0.576 in 151,836 control chromosomes in the GnomAD database, including 25,222 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.58 (25222 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.134
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -9 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.18).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.599 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.576 AC: 87362 AN: 151718 Hom.: 25212 Cov.: 31

Gnomad AFR AF: 0.544

Gnomad AMI AF: 0.658

Gnomad AMR AF: 0.568

Gnomad ASJ AF: 0.480

Gnomad EAS AF: 0.506

Gnomad SAS AF: 0.586

Gnomad FIN AF: 0.591

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.604

Gnomad OTH AF: 0.550

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.576 AC: 87406 AN: 151836 Hom.: 25222 Cov.: 31 AF XY: 0.572 AC XY: 42449 AN XY: 74160

African (AFR) AF: 0.543 AC: 22496 AN: 41418

American (AMR) AF: 0.568 AC: 8649 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.480 AC: 1663 AN: 3466

East Asian (EAS) AF: 0.507 AC: 2607 AN: 5146

South Asian (SAS) AF: 0.587 AC: 2826 AN: 4814

European-Finnish (FIN) AF: 0.591 AC: 6237 AN: 10546

Middle Eastern (MID) AF: 0.500 AC: 146 AN: 292

European-Non Finnish (NFE) AF: 0.604 AC: 41017 AN: 67902

Other (OTH) AF: 0.551 AC: 1165 AN: 2114

Alfa AF: 0.595 Hom.: 13255

Bravo AF: 0.571

Asia WGS AF: 0.537 AC: 1862 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.18
CADD	Benign	14
DANN	Benign	0.71
PhyloP100		0.13

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1478224; hg19: chr4-168437001;